Many applications in biotechnology, medicine, and pharmacology require functionalization of surfaces. Functionalization is the process of terminating a surface with a specific chemical species to produce a desired physical or chemical property at the surface. Many techniques exist for functionalizing a surface including, for example, exposure of the surface to an organosilane. This can be done using a vapor deposition process or a wet chemical process.
Furthermore, there are an increasing number of applications in which it is desirable to only functionalize selective regions of a surface or to functionalize different regions with different chemical species. One such application is the Complete Genomics DNA sequencing process. In this process, polynucleotides such as DNA macromolecules are arranged in a high-density array on a planar substrate and then imaged by four-color fluorescence microscopy. An important element in fabricating the DNA array is producing a surface that is functionalized with one type of chemical species in selected regions and is functionalized with a different chemical species outside the selected regions. More specifically, the selected regions are functionalized so that DNA macromolecules preferentially bind to these regions compared to the rest of the surface. This in turn allows for the self-assembly of arrays of DNA macromolecules when these substrates are exposed to a solution containing such macromolecules.
Devices formed as optically readable-substrates having a high feature density, e.g., attachment or deposition sites, in arrays comprising macromolecules and methods for preparing such devices and for analyzing macromolecules such as nucleic acids using such devices are described in U.S. Publication No. 2009/0270273, which is incorporated by reference herein in its entirety. The surface of the devices contain aminosilane-functionalized regions that are positively charged under certain circumstances and are capable of binding certain macromolecules such as nucleic acids, with other regions of the surface being functionalized with groups that are not able to bind to macromolecules such as nucleic acids. In the substrate fabrication process of U.S. Publication No. 2009/0270273, substrates having a trimethylsilyl monolayer and patterned regions functionalized with an aminosilane are disclosed. It has subsequently been determined that the methods disclosed in U.S. Publication No. 2009/0270273 cannot be extrapolated to produce organosilane-functionalized patterned regions having submicron dimensions as the result of several unexpected phenomena that occur under reaction conditions used to provide highly functionalized surfaces.
Improved methods for providing patterned submicron organosilane-functionalized regions on a substrate are desired.